Abstract：
CONCLUSIONS: We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.
摘要：
结论：我们报道了三种基础物种的基于图形的线粒体基因组（糖精，S.robustum和S.officinarum）首次。结果揭示了甘蔗线粒体基因组的全结构变异和进化过程。糖精属于Andropogeneae，甘蔗中的品种种类贡献了世界上近80％的糖产量。探索糖精的基因组研究，我们组装了三个基础物种的15个完整的线粒体基因组（有丝分裂基因组）（糖精，S.robustum和S.officinarum）使用Illumina和OxfordNanoporeTechnologies测序数据。根据重叠群数量和连接，将三个物种的有丝分裂基因组分为总共八种类型。这三个物种中的所有有丝分裂基因组都编码51个独特的基因，包括32个蛋白质编码，3核糖体RNA(rRNA)和16个转移RNA(tRNA)基因。通过PCR验证，揭示并证实了在S.officinarum和S.robustum的有丝分裂体中存在长重复和短重复介导的重组。此外，采用比较基因组学和细胞器基因组的系统发育分析，我们揭示了甘蔗属主要种间谱系的进化关系和历史。对S.officinarum和S.robustum之间的同源片段的系统发育分析表明，S.officinarum和S.robustum是系统发育上不同的，并且它们可能是平行的而不是驯化的。古代之间的变化(S.sinense和S.barberi)和现代栽培物种(S.杂种）可能是由涉及不同菌株的杂交引起的。最后,该项目报告了三个糖精物种的第一个基于图形的有丝分裂基因组，和结构组织的系统比较，进化过程，糖精有丝分裂基因组的全结构变异揭示了糖精有丝分裂基因组的差异特征。
